Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue (...) that they constitute an example of classificatory theory. This form of theorizing emerges from classification practices in conjunction with experimental know-how and expresses the knowledge underpinning the analysis and interpretation of data disseminated online. (shrink)

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.

This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 MIE meeting in (...) Geneva. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and (...) functionally difficult to extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is (...) a’ and ‘part of ’. (shrink)

Researchers of different calibres from phenomenology to posthumanism and beyond have outlined the processuality of the body and the environment (Alaimo 2010; Gendlin 2017), stressing the importance of changing the ontological presuppositions of the body-environment bond (Schoeller and Duanetz 2018: 131), since the existing models facilitate the alienation and intangibility of the environment, thus, leading to reduced societal awareness of the importance of environmental issues (Neimanis, Åsberg, Hedrén 2015: 73–74). In this article, I argue that in questions relating to food, (...) product-oriented ideologies dominate over process-oriented ethicality, in part, due to an embodied and lived ideology that can be best described via the concept of reactive nihilism and substance ontology. The article aims to demonstrate a necessity to rethink and recontextualize situated practices as alternatives to the prevalent ontogenealogies of the Global North. By problematizing the complimentary axis of reactive nihilism in food contexts and the genealogy of contemporary pop food “ethics”, I argue for a shift away from product-oriented ideologies and supplementation of the ontologies-we-live-by with situated alternative models. In the first part of the article, I use a genealogical approach, tracing the predominant meaning cluster encapsulated in Feuerbach’s famous expression “Man is what he eats” (Feuerbach 1846-1866, X: 5) in today’s contexts. To illustrate the leading discourses, I follow a Deleuzian understanding of the concept of “reactive nihilism” and contextualize food choices with the dominant understanding of the body in the Global North. With this discussion, I hope to provide context for the need to reconsider local ontologies as knowledge resources for the future. In the second part of the article, the framework present in the Global North is then complemented by a discussion of some local factors, to suggest ways in which global food philosophy and, particularly, lifestyle choices of food consumption could benefit from acknowledging the knowledge embedded in food consumption trends in Latvia. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of (...) kidney and skin. (shrink)

The dominant view amongst contemporary Western philosophers about the essence of a natu­ ral object is that it is constituted by its intrinsic properties. The ontological approach salient in the African philosophical tradition, in contrast, accounts for a thing’s essence by appeal to its relational properties. The Afro­relational ontology is under­developed, with the primary aim of this article being to help rectify that weakness. Specifically, this article’s aims are: to articulate an African approach to understanding the essence of a concrete, (...) natural thing in terms of its relationships; to illustrate the Afro­relational approach with the examples of the self and of water; to contrast the Afro­relational characterization of the essence of the self and of water with a typically Western construal in terms of their intrinsic properties; and finally to provide an initial defence of the Afro­relational approach, both by responding to some objections facing it and by providing some new, positive reasons to take it seriously. (shrink)

The main goal of this article is to use the epistemological framework of a specific version of Cognitive Constructivism to address Piaget’s central problem of knowledge construction, namely, the re-equilibration of cognitive structures. The distinctive objective character of this constructivist framework is supported by formal inference methods of Bayesian statistics, and is based on Heinz von Foerster’s fundamental metaphor of objects as tokens for eigen-solutions. This epistemological perspective is illustrated using some episodes in the history of chemistry concerning the definition (...) or identification of chemical elements. Some of von Foerster’s epistemological imperatives provide general guidelines of development and argumentation. (shrink)

This article discusses some continuous limit cases of Susan Haack’s crossword puzzle metaphor for the coherent development and foundation of science. The main objective of this discussion is to build a bridge between Haack’s foundherentism and the epistemological framework of objective cognitive constructivism, including its key metaphor of objects as tokens for eigen-solutions. The historical development of chemical affinity tables is used to illustrate our arguments.

Slightly modified reprint of an article first appearing in the journal _Synthesis Philosophica_ (2018).

It is common for social theorists to utilize the metaphors of ‘flow’, ‘fluidity’, and ‘liquidity’ in order to substantiate the ways in which speed and mobility form the basis for a new kind of information or network society. Yet rarely have these concepts been sufficiently theorized in order to establish their relevance or appropriateness. This article contends that the notion of flow as utilized in social theory is profoundly metaphysical in nature, and needs to be judged as such. Beginning with (...) a discussion of the accelerating timescape that characterizes the network society, it will then move on to examine three main issues with this ‘metaphysics of flux’. First, that the concept of flows unjustly privileges the process of becoming and, as a result, is unable to account for the materiality, substantiality, and agency of the objects being mobilized, and the contingency of their mediation. Second, that it posits the accelerating tendencies of capital as an ontological inevitability, thus discounting resistance to such forces. Finally, that it ignores the human faculty for reason and speculative thought in developing alternative means of political praxis. The solution, it will be argued, is not to abandon metaphysical accounts of the network society, but rather to challenge those accounts that, in exhibiting a crude empiricism, work to justify the status quo. (shrink)

This paper explores the contrast between two meanings of thinking: (i) one implied by the Cartesian and Kantian philosophy, the two thinkers that have arguably the deepest influence on the constellation of Western philosophical problems and (ii) another implied by the philosophical-anthropological project of the Brazilian anthropologist Eduardo Viveiros de Castro. The thesis here defended is that, in the Cartesian and Kantian philosophy, thinking is related to ruling and legislating over the experience through concepts, while in Viveiros de Castros' theoretical (...) enterprise, thinking is rather to explore the limits of conceptual constructions when confronted with the experience of alterity. (shrink)

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and familiarizing the reader (...) with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

Formal ontology as a main branch of metaphysics investigates categories of being. In the formal ontological approach to metaphysics, these ontological categories are analysed by ontological forms. This analysis, which we illustrate by some category systems, provides a tool to assess the clarity, exactness and intelligibility of different category systems or formal ontologies. We discuss critically different accounts of ontological form in the literature. Of ontological form, we propose a character- neutral relational account. In this metatheory, ontological forms of (...) entities are their standings in internal relations whose holding is neutral on the character of their relata. These relations are “formal ontological relations”. Entities belong to ontological categories because they stand in the same formal ontological relations. We hold a nominalist relationalism about ontological categories and forms. We conclude by showing that our metatheory is useful for understanding categorial fundamentality/non- fundamentality, different formal ontologies, and for unifying metaphysical questions. (shrink)

The gulf between philosophical and formal ontology can and should be bridged. In this Editorial, I elaborate briefly on this subject.

Ontological pluralism is the view that there are different fundamental ways of being. Trenton Merricks has recently raised three objections to combining pluralism with a generic way of being enjoyed by absolutely everything there is: first, that the resulting view contradicts the pluralist’s core intuition; second, that it is especially vulnerable to the charge—due to Peter van Inwagen—that it posits a difference in being where there is simply a difference in kind; and, third, that it is in tension with various (...) historically influential motivations for pluralism. I reply to each of these objections in turn. My replies will help to bring out the true nature of the pluralist’s basic commitments. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

This essay provides an opinionated survey of some recent developments in the literature on ontological dependence. Some of the most popular definitions of ontological dependence are formulated in modal terms; others in non-modal terms (e.g., in terms of the explanatory connective, ‘because’, or in terms of a non-modal conception of essence); some (viz., the existential construals of ontological dependence) emphasise requirements that must be met in order for an entity to exist; others (viz., the essentialist construals) focus on conditions that (...) must be satisfied in order for an entity to be the very entity it is at each time at which it exists; some are rigid, in the sense that they concern a relation between particular entities; others are generic, in the sense that they involve only a relation between an entity and some entities or other, which bear certain characteristics. I identify three potential measures of success with respect to which these different definitions of ontological dependence can be evaluated and consider the question of how well they in fact meet these desiderata. I end by noting that certain challenges face even the most promising essentialist construals of ontological dependence. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

Standard approaches to ontological simplicity focus either on the number of things or types a theory posits or on the number of fundamental things or types a theory posits. In this paper, I suggest a ground-theoretic approach that focuses on the number of something else. After getting clear on what this approach amounts to, I motivate it, defend it, and complete it.

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those (...) who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

The aim of this paper is to summarize a particular approach of doing metaphysics through physics - the primitive ontology approach. The idea is that any fundamental physical theory has a well-defined architecture, to the foundation of which there is the primitive ontology, which represents matter. According to the framework provided by this approach when applied to quantum mechanics, the wave function is not suitable to represent matter. Rather, the wave function has a nomological character, given that its role in (...) the theory is to implement the law of evolution for the primitive ontology. (shrink)

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where (...) ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the (...) different token ontologies. In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)

In many different ontological debates, anti-arbitrariness considerations push one towards two opposing extremes. For example, in debates about mereology, one may be pushed towards a maximal ontology (mereological universalism) or a minimal ontology (mereological nihilism), because any intermediate view seems objectionably arbitrary. However, it is usually thought that anti-arbitrariness considerations on their own cannot decide between these maximal or minimal views. I will argue that this is a mistake. Anti-arbitrariness arguments may be used to motivate a certain popular thesis in (...) the philosophy of mathematics that rules out the maximalist view in many different ontological debates. (shrink)

The ontology of Local Quantum Physics, Rudolf Haag’s framework for relativistic quantum theory, is reviewed and discussed. It is one of spatiotemporally localized events and unlocalized causal intermediaries, including the elementary particles, which come progressively into existence in accordance with a fundamental arrow of time. Haag’s conception of quantum theory is distinguished from others in which events are also central, especially those of Niels Bohr and John Wheeler, with which it has been compared.

The discipline of applied ethics already has a certain familiarity in the Anglo-Saxon world, above all through the work of Peter Singer. Applied ethics uses the tools of moral philosophy to resolve practical problems of the sort which arise, for example, in the running of hospitals. In the University at Buffalo (New York) there was organized on April 24-25 1998 the world's first conference on a new, sister discipline, the discipline of applied ontology. Applied ontologists seek to apply ontological tools (...) to solving practical problems of the sort which arise in various extra-philosophical domains, including law and government administration. (shrink)

In this chapter, I examine Lewis's ideas about ontological innocence, ontological commitment and double-counting, in his discussion of composition as identity in Parts of Classes. I attempt to understand these primarily as epistemic or methodological claims: how far can we get down this route without adopting radical metaphysical theses about composition as identity?

Easy Ontology (EO), defended in several recent works by Amie Thomasson, and based on Carnap’s famous deflationism about metaphysics, is the view that many ontological questions, like ‘Are there numbers?’, are at bottom easy, at least when taken in their “internal” sense. Both Carnap and Thomasson take for granted that serious metaphysicians therefore cannot plausibly be interpreted as asking internal questions. Thus, they think they are committed to finding some alternative, special interpretation of metaphysicians’ utterances. I argue that none of (...) the alternative interpretations proposed in the literature are viable. More importantly, I argue that Carnap and Thomasson are wrong about this commitment. EO should instead be coupled with the view that metaphysicians ask internal questions, yet have the false belief that they can be answered only through metaphysical speculation. This is a significant modification of EO, in which the notion of an “external question” plays no role, and which results in a simpler and more plausible theory. (shrink)

This article serves to explore the historical development of the ontological argument from Anselm to Present. Initially, the main goal is to introduce the lay reader to one of the most perplexing arguments for the theistic conception of God. Logically, this is an a priori argument, similar to one of a mathematical proof. Oddly, the argument has sort of fallen out of place in contemporary philosophy, apart from a reboot from Alvin Plantinga. The goal is to illustrate that the initial (...) argument as stated by Anselm seems to be an unsolved problem in philosophical inquiry. (shrink)

Because climate change can be seen as the blind spot of contemporary philosophy of technology, while the destructive side effects of technological progress are no longer deniable, this article reflects on the role of technologies in the constitution of the (post)Anthropocene world. Our first hypothesis is that humanity is not the primary agent involved in world-production, but concrete technologies. Our second hypothesis is that technological inventions at an ontic level have an ontological impact and constitutes world. As we object to (...) classical philosophers of technology like Ihde and Heidegger, we will sketch the progressive contribution of our conceptuality to understand the role of technology in the Anthropocene world. Our third hypothesis is that technology has emancipatory potential and in this respect, can inaugurate a post-Anthropocene World. We consider these three hypotheses to develop a philosophical account of the ontology of technology beyond an abstract and deterministic understanding. This concept enables us to philosophically reflect on the role of technology in the Anthropocene World in general, and its contribution to the transition to the post-Anthropocene World in particular. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are (...) relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

This paper is an exposition and comparison between two views concerning fundamental ontology in the context of the Mind-Body Problem: physicalism and emergent property dualism. I assess the pros and cons of each position and argue that physicalism provides an overall more plausible metaphysics.

Ontological pluralism is the view that there are different ways of being. Historically, ways of being are aligned with the ontological categories. This paper is about to investigate why there is such a connection, and how it should be understood. Ontological pluralism suffers from an objection, according to which ontological pluralism collapses into ontological monism, i.e., there is only one way to be. Admitting to ontological categories can save ontological pluralism from this objection if ways of being ground ontological categories. (...) -/- . (shrink)

The origin of the concept of “emotional sharing” can be traced back to the first edition of Sympathiebuch [1913/23], in which Max Scheler paved the way to a phenomenology of emotions and to social ontology. The importance of his findings is evident: consider the central role of emotional sharing in Michael Tomasello’s analysis and the lively debate on social ontology and collective intentionality.

Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the pluralist (...) are mere notational variants of those proposed by the monist, in which case the debate between the two positions would not seem to be substantive. Jason Turner has given an ingenious response to this worry, in terms of a principle that he calls ‘logical realism’. This paper offers a counter-response on behalf of the ‘notationalist’. I argue that, properly applied, the principle of logical realism is no threat to the claim that the languages in question are notational variants. Indeed, there seems to be every reason to think that they are. (shrink)

Quine's views on ontology and naturalism are well-known but rarely considered in tandem. According to my interpretation the connection between them is vital. I read Quine as a global epistemic structuralist. Quine thought we only ever know objects qua solutions to puzzles about significant intersections in observations. Objects are always accessed descriptively, via their roles in our best theory. Quine's Kant lectures contain an early version of epistemic structuralism with uncharacteristic remarks about the mental. Here Quine embraces mitigated anomalous monism, (...) allowing introspection and the availability in principle of full physical descriptions of the perceptual states which get science off the ground. Later versions abandon these ideas. My epistemic-structural interpretation explains why. I argue first-personal introspective access to mental states is incompatible with global epistemic structuralism. (shrink)

I will here present a number of problems concerning the idea that there is ontological vagueness, and the related claim that appeal to this idea can help solve some vagueness-related problems. A theme underlying the discussion will be the distinction between vagueness specifically and indeterminacy more generally (and, relatedly, the distinction between ontological vagueness and ontological indeterminacy). Even if the world is somehow ontologically indeterminate it by no means follows that it is, properly speaking, ontologically vague.1..

The thesis of methodological individualism in social science is commonly divided into two different claims—explanatory individualism and ontological individualism. Ontological individualism is the thesis that facts about individuals exhaustively determine social facts. Initially taken to be a claim about the identity of groups with sets of individuals or their properties, ontological individualism has more recently been understood as a global supervenience claim. While explanatory individualism has remained controversial, ontological individualism thus understood is almost universally accepted. In this paper I argue (...) that ontological individualism is false. Only if the thesis is weakened to the point that it is equivalent to physicalism can it be true, but then it fails to be a thesis about the determination of social facts by facts about individual persons. Even when individualistic facts are expanded to include people’s local environments and practices, I shall argue, those still underdetermine the social facts that obtain. If true, this has implications for explanation as well as ontology. I first consider arguments against the local supervenience of social facts on facts about individuals, correcting some flaws in existing arguments and affirming that local supervenience fails for a broad set of social properties. I subsequently apply a similar approach to defeat a particularly weak form of global supervenience, and consider potential responses. Finally, I explore why it is that people have taken ontological individualism to be true. (shrink)

The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species, race, memory, intelligence, depression, or obesity are true or false relative to the choice of a biological, psychological, or medical ontology. Second, I show that ontological choices often depend on non-epistemic values. On the basis of (...) these premises, I argue that it is often neither possible nor desirable to evaluate scientific statements independently of non-epistemic values. Finally, I suggest that considerations of ontological choices do not only challenge the value-free ideal but also help to specify positive roles of non-epistemic values in an often neglected area of scientific practice. (shrink)

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts in (...) terms of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...) similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines (...) and attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)